# Hail hl.linear\_mixed\_model out of memory

**URL:** <https://discuss.hail.is/t/hail-hl-linear-mixed-model-out-of-memory/2126>\
**Category:** Hail Query & hailctl\
**Created:** [July 10, 2021, 5:50pm UTC](https://discuss.hail.is/t/hail-hl-linear-mixed-model-out-of-memory/2126 "2021-07-10T17:50:05Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![qinfinn](https://avatars.discourse-cdn.com/v4/letter/q/e47c2d/32.png) [@qinfinn](https://discuss.hail.is/u/qinfinn)\
**Post date:** [July 10, 2021, 5:50pm UTC](https://discuss.hail.is/t/hail-hl-linear-mixed-model-out-of-memory/2126/1 "2021-07-10T17:50:05Z")

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Hi Hail team

I am running a global linear mixed model with 480k individuals and 42k variants (marker list). The matrix table is partitioned to 100 blocks.

The code I am using is:  
filtered\_mt=filtered\_mt.repartition(100)  
model, \_ = hl.linear\_mixed\_model(  
y=filtered\_mt.pheno.BMI,  
x=[1],  
z\_t=filtered\_mt.GT.n\_alt\_alleles(),  
p\_path=‘output/p.bm’)

I have also tried different partitions, e.g. 10 and 500 blocks. Also I tried various settings for SPARK, but alway return the out of memory error.  
e.g.  
setting 1:  
–conf spark.executor.cores=5   
–conf spark.executor.memoryOverhead=6g   
–conf spark.executor.memory=19g   
–conf spark.executor.instances=17

setting 2:  
–conf spark.executor.cores=4   
–conf spark.executor.memoryOverhead=20g   
–conf spark.executor.memory=40g   
–conf spark.executor.instances=6

I have pasted the error message blow.

Many thanks.

Best wishes,  
Qin

Traceback (most recent call last):  
File “”, line 5, in   
File “”, line 2, in linear\_mixed\_model  
File “/local/apps/anaconda-python36/lib/python3.6/site-packages/hail/typecheck/check.py”, line 577, in wrapper  
return _original\_func(\*args, \*\*kwargs_)  
File “/local/apps/anaconda-python36/lib/python3.6/site-packages/hail/methods/statgen.py”, line 1070, in linear\_mixed\_model  
model, p = LinearMixedModel.from\_random\_effects(y\_nd, x\_nd, z\_bm, p\_path, overwrite)  
File “”, line 2, in from\_random\_effects  
File “/local/apps/anaconda-python36/lib/python3.6/site-packages/hail/typecheck/check.py”, line 577, in wrapper  
return _original\_func(\*args, \*\*kwargs_)  
File “/local/apps/anaconda-python36/lib/python3.6/site-packages/hail/stats/linear\_mixed\_model.py”, line 1081, in from\_random\_effects  
u, s0, \_ = z.svd(complexity\_bound=complexity\_bound)  
File “”, line 2, in svd  
File “/local/apps/anaconda-python36/lib/python3.6/site-packages/hail/typecheck/check.py”, line 577, in wrapper  
return _original\_func(\*args, \*\*kwargs_)  
File “/local/apps/anaconda-python36/lib/python3.6/site-packages/hail/linalg/blockmatrix.py”, line 2403, in svd  
return self.\_svd\_gramian(compute\_uv)  
File “”, line 2, in \_svd\_gramian  
File “/local/apps/anaconda-python36/lib/python3.6/site-packages/hail/typecheck/check.py”, line 577, in wrapper  
return _original\_func(\*args, \*\*kwargs_)  
File “/local/apps/anaconda-python36/lib/python3.6/site-packages/hail/linalg/blockmatrix.py”, line 2415, in \_svd\_gramian  
.sparsify\_triangle(lower=True, blocks\_only=True)  
File “”, line 2, in to\_numpy  
File “/local/apps/anaconda-python36/lib/python3.6/site-packages/hail/typecheck/check.py”, line 577, in wrapper  
return _original\_func(\*args, \*\*kwargs_)  
File “/local/apps/anaconda-python36/lib/python3.6/site-packages/hail/linalg/blockmatrix.py”, line 1205, in to\_numpy  
self.tofile(uri)  
File “”, line 2, in tofile  
File “/local/apps/anaconda-python36/lib/python3.6/site-packages/hail/typecheck/check.py”, line 577, in wrapper  
return _original\_func(\*args, \*\*kwargs_)  
File “/local/apps/anaconda-python36/lib/python3.6/site-packages/hail/linalg/blockmatrix.py”, line 1177, in tofile  
Env.backend().execute(BlockMatrixWrite(self.\_bmir, writer))  
File “/local/apps/anaconda-python36/lib/python3.6/site-packages/hail/backend/py4j\_backend.py”, line 98, in execute  
raise e  
File “/local/apps/anaconda-python36/lib/python3.6/site-packages/hail/backend/py4j\_backend.py”, line 74, in execute  
result = json.loads(self.\_jhc.backend().executeJSON(jir))  
File “/opt/cloudera/parcels/CDH-6.3.3-1.cdh6.3.3.p4757.13086441/lib/spark/python/lib/py4j-0.10.7-src.zip/py4j/java\_gateway.py”, line 1257, in **call**  
File “/local/apps/anaconda-python36/lib/python3.6/site-packages/hail/backend/py4j\_backend.py”, line 32, in deco  
‘Error summary: %s’ % (deepest, full, hail. **version** , deepest), error\_id) from None  
hail.utils.java.FatalError: OutOfMemoryError: Java heap space

Java stack trace:  
java.lang.OutOfMemoryError: Java heap space  
at scala.reflect.ManifestFactory$$anon$12.newArray(Manifest.scala:141)  
at scala.reflect.ManifestFactory$$anon$12.newArray(Manifest.scala:139)  
at breeze.linalg.DenseMatrix$mcD$sp.toArray$mcD$sp(DenseMatrix.scala:129)  
at is.hail.utils.richUtils.RichDenseMatrixDouble$.toCompactData$extension(RichDenseMatrixDouble.scala:90)  
at is.hail.utils.richUtils.RichDenseMatrixDouble$.exportToDoubles(RichDenseMatrixDouble.scala:53)  
1(InterpretNonCompilable.scala:16)  
at is.hail.expr.ir.InterpretNonCompilable$.is$hail$expr$ir$InterpretNonCompilable$$rewrite$1(InterpretNonCompilable.scala:53)  
at is.hail.expr.ir.InterpretNonCompilable$.apply(InterpretNonCompilable.scala:58)  
at is.hail.expr.ir.lowering.InterpretNonCompilablePass$.transform(LoweringPass.scala:67)  
at is.hail.expr.ir.lowering.LoweringPass$$anonfun$apply$3$$anonfun$1.apply(LoweringPass.scala:15)  
at is.hail.expr.ir.lowering.LoweringPass$$anonfun$apply$3$$anonfun$1.apply(LoweringPass.scala:15)  
at is.hail.utils.ExecutionTimer.time(ExecutionTimer.scala:81)  
at is.hail.expr.ir.lowering.LoweringPass$$anonfun$apply$3.apply(LoweringPass.scala:15)  
at is.hail.expr.ir.lowering.LoweringPass$$anonfun$apply$3.apply(LoweringPass.scala:13)  
at is.hail.utils.ExecutionTimer.time(ExecutionTimer.scala:81)  
at is.hail.expr.ir.lowering.LoweringPass$class.apply(LoweringPass.scala:13)  
at is.hail.expr.ir.lowering.InterpretNonCompilablePass$.apply(LoweringPass.scala:62)  
at is.hail.expr.ir.lowering.LoweringPipeline$$anonfun$apply$1.apply(LoweringPipeline.scala:14)  
at is.hail.expr.ir.lowering.LoweringPipeline$$anonfun$apply$1.apply(LoweringPipeline.scala:12)  
at scala.collection.IndexedSeqOptimized$class.foreach(IndexedSeqOptimized.scala:33)  
at scala.collection.mutable.WrappedArray.foreach(WrappedArray.scala:35)  
at is.hail.expr.ir.lowering.LoweringPipeline.apply(LoweringPipeline.scala:12)  
at is.hail.expr.ir.CompileAndEvaluate$.\_apply(CompileAndEvaluate.scala:28)  
at is.hail.backend.spark.SparkBackend.is$hail$backend$spark$SparkBackend$$\_execute(SparkBackend.scala:360)  
at is.hail.backend.spark.SparkBackend$$anonfun$execute$1.apply(SparkBackend.scala:344)  
at is.hail.backend.spark.SparkBackend$$anonfun$execute$1.apply(SparkBackend.scala:341)  
at is.hail.expr.ir.ExecuteContext$$anonfun$scoped$1.apply(ExecuteContext.scala:25)  
at is.hail.expr.ir.ExecuteContext$$anonfun$scoped$1.apply(ExecuteContext.scala:23)  
at is.hail.utils.package$.using(package.scala:618)

Hail version: 0.2.62-84fa81b9ea3d  
Error summary: OutOfMemoryError: Java heap space

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<div class="post-metadata">

**Author:** ![tpoterba](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/tpoterba/32/61_2.png) [@tpoterba](https://discuss.hail.is/u/tpoterba)\
**Post date:** [July 14, 2021, 10:24pm UTC](https://discuss.hail.is/t/hail-hl-linear-mixed-model-out-of-memory/2126/2 "2021-07-14T22:24:58Z")

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Hi! I’m sorry you’re running into these issues. Unfortunately LMM functionality in Hail is very poorly maintained, and you’ll almost certainly have a better experience using Hail for QC then exporting to a BGEN/VCF to use tools like BOLT-LMM or SAIGE to run the statistical analysis.